Ex Parte Mandecki

Patent Trial and Appeal BoardSep 17, 2012

10871260 (P.T.A.B. Sep. 17, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 10/871,260 06/18/2004 Wlodek Mandecki MAND001 9885 39731 7590 09/17/2012 Moser Taboada / Art Jackson 1030 BROAD STREET, SUITE 203 SHREWSBURY, NJ 07702 EXAMINER STAPLES, MARK ART UNIT PAPER NUMBER 1637 MAIL DATE DELIVERY MODE 09/17/2012 PAPER Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE __________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte WLODEK MANDECKI __________ Appeal 2011-007338 Application 10/871,260 Technology Center 1600 __________ Before DONALD E. ADAMS, ERIC GRIMES, and JEFFREY N. FREDMAN, Administrative Patent Judges. GRIMES, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134 involving claims to an assay method, which the Examiner has rejected for obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We reverse. STATEMENT OF THE CASE The Specification discloses “an assay method for acquiring sequence information about a single nucleic acid molecule” (Spec. 5, ¶ 10). The method is disclosed as having several applications (see id. at 17, ¶ 55), including nucleic acid sequencing (id. at 17, ¶ 57), and is said to allow Appeal 2011-007338 Application 10/871,260 2 sensing of a nucleic acid sequence with high nucleotide specificity, without resulting in a fluorescent label being incorporated into the nucleic acid (id. at 4-5, ¶¶ 8-9). Claims 33 and 35-52 are on appeal. Claim 33 is representative and reads as follows: 33. An assay method for acquiring information on the relative locations of one or more codons on a single ribonucleic acid, the method comprising: contacting components including a ribosomal particle comprising a ribosome and the ribonucleic acid with a complex comprising moieties that are aa1-tRNA, EF-Tu and GTP or a functional analog, wherein at least one said moiety is labeled with a fluorescent molecule (label one), wherein aa1- tRNA is a tRNA for first amino acid aa1 that is charged with aa1; providing, in conjunction with the contacted components, a ribosomal translation component mixture; generating multiple fluorescent signals over time from label one in correlation with (i) incorporations of aa1 into protein pursuant to translation of the ribonucleic acid directed by the ribosomal particle and (ii) resultant separations of the labeled moiety from the complex; and detecting in real time the fluorescent signals from label one over a course of time, the detected signals generated from a single said ribosomal particle and result from the separations of the labeled moiety from the complex, to provide information on the relative positions of codons for aa1 on the ribonucleic acid. Claim 51, the only other independent claim, includes all of the steps of claim 33 with either identical or narrower limitations, as well as additional steps (see Appeal Br. 46-47 (Claims Appendix)). Appeal 2011-007338 Application 10/871,260 3 The Examiner has rejected all of the claims on appeal under 35 U.S.C. § 103(a) as obvious based on Smilansky,1 Watson,2 Shipwash,3 and Truong4 (Answer 4).5 The Examiner finds that Smilansky teaches many of the limitations of claim 33 (id. at 5-7), including “labeling tRNA and elongation factor EF-TU and a GTP molecule (see paragraph 211)” (id. at 7), but “does not specifically teach detecting fluorescent signals which result from physical intermolecular separations of the labeled moiety in the complex from the complex” (id. at 8). The Examiner finds that Watson teaches labeling the tRNA and GTP molecules in a ternary complex6 (id. at 7), and teaches that binding of the labeled tRNA to the EF-Tu/labeled GTP complex increased the intensity of the tRNA label signal, “which necessarily means . . . a decrease in fluorescein intensity results from the separation of EF-TuGTP from [labeled tRNA], as claimed” (id.). 1 Smilansky, Patent Application Publication, US 2006/0228708 A1, Oct. 12, 2006 2 Bonnie S. Watson et al., Macromolecular Arrangement in the Aminoacyl- tRNA-Elongation Factor Tu-GTP Ternary Complex. A Fluorescence Energy Transfer Study, 34 BIOCHEMISTRY 7904-7912 (1995). 3 Shipwash, US 6,846,638 B2, Jan. 25, 2005. 4 Kevin Truong et al., The use of FRET imaging microscopy to detect protein-protein interactions and protein conformational changes in vivo, 11 CURRENT OPINION IN STRUCTURAL BIOLOGY 573-578 (2001) 5 The Examiner also cites Selvin, Fluorescence Resonance Energy Transfer, 346 METH. ENZYMOL. 300-334 (1995), in the statement of the rejection (Answer 4), but relies on its teachings only with respect to claims that are narrower than claim 33. Therefore, we will not discuss Selvin. 6 A ternary complex consists of an amino acid-charged tRNA, elongation factor Tu (EF-Tu), and GTP (Spec. 38, ¶ 112). Appeal 2011-007338 Application 10/871,260 4 The Examiner finds that Shipwash discloses a method of analyzing ribonucleic acid (id. at 12) and teaches that “one or both of the amino acyl tRNA or the elongation factor is labeled with a fluorescent label to facillitate [sic] detection of the ternary complex” (id.). The Examiner finds that Truong teaches “methods for acquiring information [on] the relative locations of protein moieties in a protein-protein complex” using fluorescence resonance energy transfer (FRET) (id. at 15). The Examiner concludes that it would have been obvious to modify the real time methods for acquiring positional information of a codon on a single ribonucleic acid of Smilansky as evidenced by Watson et al. by detecting signals which result from separation of a EF-Tu moiety from the EF-Tu complex as suggested by Smilansky, Watson et al., Shipwash, and Truong et al. with a reasonable expectation of success. (Id. at 15-16). The Examiner finds that motivation to do so is provided by Smilansky, Watson et al., and Shipwash who teach that the EF-TU complex can be detected by the distance separation including intramolecular separation of the two labels of a fluorescence energy transfer pair (FRET) where those labels are on the EF-TU complex and that this can be used to acquire information on codon positions. (Id. at 16.) Appellant argues that the cited references do not support the Examiner’s assertion that they would have suggested, in the Examiner’s words, “detecting signals which result from separation of a EF-Tu moiety from the EF-Tu complex” (Appeal Br. 20-21). We agree with Appellant that the Examiner has not persuasively shown that the cited references would have made it obvious to modify Smilansky’s method by detecting signals that result from separation of an Appeal 2011-007338 Application 10/871,260 5 EF-Tu moiety from an EF-Tu/GTP/charged tRNA complex. Smilansky discloses a method for monitoring protein synthesis (Smilansky 3, ¶ 26) in which a label on the ribosome (id. at 3, ¶ 29) interacts with a label (“synthesis marker”) that allows detection of which tRNA is currently being processed by the ribosome (id. at 3, ¶ 27). Smilansky describes embodiments in which the ribosomal label interacts with a label on a specific tRNA (“R-T labeling”; id. at 13, ¶¶ 183-185), or with a label on the amino acid itself (“R-A labeling”; id. at 13, ¶¶ 187-188), or with a second label on the ribosome (“R-R labeling”; id. at 13, ¶¶ 190-191). Contrary to the Examiner’s finding (Answer 7), Smilansky does not describe an embodiment that involves labeling EF-Tu. The Examiner cites Smilansky’s paragraph 211 for that disclosure but that paragraph refers to labeling a tRNA molecule, and states only (with respect to EF-Tu) that “[a]s a tRNA molecule docks onto (binds to) the ribosome- mRNA complex, it is bound with elongation factor EF-TU and a GTP molecule. Tagging should also be compatible with this complex.” (Smilansky, ¶ 211.) Watson also does not disclose labeling of EF-Tu. Watson describes a fluorescence resonance energy transfer (FRET) experiment designed to measure the distance between the GTP and tRNA molecules in a ternary complex based on the amount of energy transferred between labels attached to each of the molecules (Watson 7904 (abstract)). Watson therefore provides evidence that the amount of energy transferred between members of a FRET pair varies depending on the distance separating them, but it Appeal 2011-007338 Application 10/871,260 6 provides no reason to modify Smilansky’s method to include a label on EF- Tu. Truong discloses that FRET can be used to detect the formation of a protein-protein complex (intermolecular FRET) or the conformational change of a single protein (intramolecular FRET) (Truong 574, Fig. 1). The Examiner has pointed to no disclosure in Truong that is specific to the protein translation process, ribosomes, or components of a ternary complex. Shipwash does disclose “a preferred embodiment [in which] one or both of the amino acyl tRNA or the elongation factor is labeled with a fluorescent label to facillitate [sic] detection of the ternary complex” (Shipwash, col. 85, ll. 62-64, (emphasis added)). However, the method in which Shipwash uses the labeled ternary complex is very different from Smilansky’s method. Shipwash discloses “methods for rapid biomolecular recognition based detection of amino acids in a sample” (Shipwash, col. 1, ll. 12-14). Shipwash’s method is thus directed to detecting amino acids, not “acquiring information on the relative locations of one or more codons” (Answer 12), as the Examiner found. “The basis of [Shipwash’s] method is that each of the 20 synthetases and/or a tRNA specific for a different amino acid is separated spatially or differentially labeled. . . . Each separately positioned synthetase or tRNA will signal its cognate amino acid.” (Shipwash, abstract.) That is, “the primary protein amino acids . . . are attached to their corresponding or cognate tRNAs by the corresponding or cognate aminoacyl-tRNA synthetase” (id. at col. 6, ll. 15-20). Since “EF-Tu binds to an aminoacyl Appeal 2011-007338 Application 10/871,260 7 tRNA with a Kd of about 10-9 M but not a tRNAs [sic] lacking an amino acyl moiety . . . known ligand assays can then be used to monitor the concentration of amino acids in a sample” (id. at col. 7, ll. 49-55). Shipwash describes a “method for the detection of one or more primary protein amino acids in a sample by biomolecular recognition wherein the coresponding [sic] aminoacyl-tRNA synthetases combine with the primary protein amino acid to yield a detectable product” (id. at col. 84, ll. 49-53). The method involves contacting a “sample with an amount of the aminoacyl-tRNA synthetase specific to the primary protein amino acid sufficient to form a detectable product and then detecting the detectable product” (id. at col. 84, l. 65 to col. 85, l. 1). “In a further embodiment of the method, an aminoacyl-tRNA is complexed with an elongation factor and the complex of the aminoacyl- tRNA with the elongation factor is determined” (id. at col. 85, ll. 27-29). In this context, Shipwash discloses that “[i]n a preferred embodiment one or both of the aminoacyl tRNA or the elongation factor is labeled with a fluorescent label to facillitate [sic] detection of the ternary complex” (id. at col. 85, ll. 62-64). Then the “fluorescent probe is captured on the microarray via formation of the ternary complex above, the unbound material is washed away and the fluorescence bound to each element in the captured portion is visualized by fluorescence detection” (id. at col. 86, ll. 4-8). Shipwash’s disclosure of labeled EF-Tu is thus in the context of an assay to detect the formation of a ternary complex consisting of an amino acid-charged tRNA, GTP, and EF-Tu by capturing labeled ternary complexes on a microarray and detecting the fluorescent label, whether it is Appeal 2011-007338 Application 10/871,260 8 attached to the charged tRNA or to EF-Tu or both. In Shipwash’s assay, the location of the label is unimportant to detection of the ternary complex, because the ternary complex is formed only if the specific amino acid of interest is present in the sample. By contrast, Smilansky’s assay depends on a label that is located on a component that is specific for the specific amino acid of interest: either the amino acid itself (R-A labeling), its cognate tRNA (R-T labeling), or a part of the ribosome that specifically reacts to the codon corresponding to the amino acid of interest (R-R labeling). In each case, detection of a fluorescent signal depends on proximity between the ribosomal label and the label specific to the amino acid of interest (see Smilansky 13-14, ¶¶ 186, 189, 192). The Examiner’s conclusion that it would have been obvious to modify Smilansky’s method “by detecting signals which result from separation of a EF-Tu moiety from the EF-Tu complex as suggested by Smilansky, Watson et al., Shipwash, and Truong et al.” (Answer 16) is not supported by the evidence. Specifically, the Examiner has not persuasively explained why Shipwash’s disclosure of labeled EF-Tu for detection of a ternary complex itself would have made it obvious to modify Smilansky’s assay methods by labeling EF-Tu, when EF-Tu binds non-discriminately to charged tRNAs, and Smilansky’s method depends on amino acid-specific labeling. The Examiner finds that [f]urthermore motivation to do so is provided by Shipwash who teach many embodiments both of FRET label pairs and of a single fluorescent label and their uses with EF-TU complexes including real time monitoring of separation of a labeled EF-TU Appeal 2011-007338 Application 10/871,260 9 protein moiety from the complex in order to detect the codon on the charged tRNA of the complex. (Answer 16.) However, although the Examiner points to a general discussion of FRET assays in Shipwash (id. at 13), he does not identify any disclosure in the reference of FRET label pairs used to detect separation of labeled EF-Tu from a ternary complex (see id. at 12-14). Finally, the Examiner finds that “[e]ven further motivation do so is provided by Truong et al. who teach that the separation and/or binding of protein moieties in complexes can be readily detected by FRET pair labels” (Answer 16). The Examiner concludes that it would have been further obvious “to substitute the intermolecular separation of FRET labeled moieties in a complex as taught by Truong et al. for the intramolecular separation of EF-TU moieties for detecting codon incorporation as taught by Smilansky to arrive at the claimed invention” (id.). We again disagree with the Examiner’s conclusion. As discussed above, Truong is nothing more than a general discussion of using FRET to detect the interaction between two proteins, or two parts of the same protein. The Examiner has not persuasively explained why Truong’s generic disclosure would have provided a reason to modify Smilansky’s assay as required by the claims on appeal. In addition, the Examiner’s apparent finding that Smilansky teaches “the intramolecular separation of EF-TU moieties for detecting codon incorporation” (Answer 16) is not supported by the evidence. First, translation does not involve “intramolecular separation of EF-TU moieties,” and second, Smilansky’s methods do not depend on detecting separation of EF-Tu from anything; they depend on detecting the Appeal 2011-007338 Application 10/871,260 10 proximity between a label on the ribosome and a label on an amino acid- specific moiety. SUMMARY The Examiner has not shown that the method of claim 33 would have been obvious based on the cited references. We therefore reverse the rejection of claim 33, as well as claims 35-52, which are narrower than claim 33. REVERSED lp